Diarrheal diseases are serious global public health problem (Guerrant et al., 2002). The World Health Organization’s Global Burden of Disease study reported that diarrheal diseases were the seventh leading cause of death in 2010, worldwide (Lozano et al., 2012). In 2015, diarrheal diseases caused globally 1.32 million deaths (GBD 2015 Mortality and Causes of Death Collaborators, 2016). In China, about 700000 cases of diarrheal diseases are reported annually (Zhu et al., 2008). Among the diarrheal diseases, acute diarrhea occurs most commonly and has most serious impact on human health in terms of mortality and medical costs (Das and Bhutta, 2016; Riddle et al., 2016).

Most of the causative agents of acute diarrheas are bacteria and viruses, among which Salmonella, Shigella, Vibrio parahaemolyticus, rotavirus, and norovirus account for a largest proportion of cases worldwide (Farthing et al., 2013). Studies report that the prevalence and composition of diarrheal pathogens varies from region to region. For example, rotavirus and diarrheagenic Escherichia coil (DEC) were the leading pathogens in Bangladesh in 2011 based on culture, polyacrylamide gel electrophoresis (PAGE) and Multiplex polymerase chain reaction (PCR) detections (Kabir et al., 2012). Rotavirus and Shigella were the main cause of diarrhea in western Kenya from 2009 to 2011 by culture and enzyme immunoassay (Swierczewski et al., 2013), while norovirus and Clostridium difficile were the most commonly detected pathogens in Australia in 2007 by culture, ELISA, reverse-transcription PCR (RT-PCR) and immunochromatography (Huhulescu et al., 2009). Calicvirus, rotavirus and Campylobacter jejuni were the most commonly detected pathogens in a Nordic country epidemiological survey from 2003 to 2007 by culture, RT-PCR and immunochromatography (Hilmarsdottir et al., 2012), while norovirus and Salmonella were the major pathogens for foodborne illness in the United States from 2000 to 2008 reported in a data estimate research (Scallan et al., 2011). However, the detailed etiological reports of acute diarrhea in a specific area are rare and these studies should be conducted to ensure proper epidemiological control and effective treatment, especially in densely populated areas. Shanghai is the largest urban agglomeration, which encompasses over 50 million people living at the highest population density in the world and experiencing huge amount of national and international traffic. From this perspective epidemiological surveillance of this area is particularly important to the global health.

Increasing occurrence of pathogenic V. parahaemolyticus and Salmonella promoted studies dissecting genetic typing of these pathogens and associations between their virulence factors and their pathogenicity (Scallan et al., 2011). The pathogenesis of V. parahaemolyticus is mainly attributed to the presence of thermostable direct hemolysin (TDH), thermolabile hemolysin (TLH) and TDH-related hemolysin (TRH), which are encoded by the tdh, tlh, and trh genes, respectively (Taniguchi et al., 1986). The pathogenicity of Salmonella is linked to a variety of virulence factors present in the chromosomal Salmonella pathogenicity islands (SPIs) and the Salmonella plasmid virulence (SPV) operon (Groisman and Ochman, 1996, 1997). Except for bacteria gastroenteritis, viral gastroenteritis is also one of the most common illnesses in human worldwide (Mo et al., 2015). Previous studies showed that the pathogenesis of viruses was due to viral genome types and environmental factors (Aly et al., 2007; Vidovic et al., 2011). Thus, analysis of the specific-virulence related genes is needed for better understanding the mechanisms of pathogenicity and to predict possible risks and outcomes of infection with various substrains.

Since, bacterial pathogens are the major cause of diarrheal diseases, ever-increasing antibiotic resistance is one of the most serious consideration in choice for their treatment (Arias and Murray, 2009). Thus analysis of antibiotic resistance is the crucial component of bacteriological diagnostics. Epidemiological studies of several hospitals in different cities of China revealed that resistance especially, multi-drug or pan-drug resistance kept increasing with the alarming rate (Gong et al., 2017; He et al., 2017; Hu et al., 2017; Yang et al., 2017). Thus, the investigation of antibiotic resistance spectrum of diarrheal bacteria may provide important information for healthcare providers in proper treatments and taking measures to reduce drug resistance of bacteria.

Finally, studies increasingly demonstrated the associations between most prevalent genotypes with particular virulence attributes and types of antimicrobial drug resistance in the clinical bacterial isolates. Such relationships were reported in Listeria monocytogenes, Klebsiella pneumoniae, V. parahaemolyticus and Salmonella (Campioni et al., 2012; Luo et al., 2014; Wu et al., 2016; Li et al., 2017). However, the study of genetic diversity of enteric bacterial pathogens has become a great challenge due to the high rates of recombination and mutation resulting from rapid selection and microevolution of prevalent microbial sub-strains (Denamur and Matic, 2006). Compared to other typing methods, including serotyping and pulsed-field gel electrophoresis (PFGE), MLST was proposed to provide one of the most effective tools for investigating the prevalence and genetic diversity of pathogenic bacteria at multiple levels (Achtman et al., 2012; Jones et al., 2012).

The aim of our study was to analyze the clinical epidemiology of infectious acute diarrhea, explore the seasonality and distribution of the pathogens and to gain insight into antimicrobial resistance, prevalence of virulence genes and genetic diversities. Considering Shanghai is one of the greatest international metropolis in the world with a huge flow of people, the study of the epidemiological characteristics and pathogen features of acute diarrhea have important local and global implications in understanding pathogens epidemiology and evolution.

Shanghai is a “gateway to China” and the largest agglomeration worldwide experiencing huge amount of national and international traffic. From the epidemiological stand point updates on the epidemiological status need to be reported and recorded on regular basis. This in comparison with other major urban centers in the world will allow to better track the spread of GI infections and to observe local and global microevolution of GI pathogens. In this study, microbiological surveillance of 412 stool specimens from total of 2059 diarrhea patients has been conducted between January and December in 2016 in Shanghai. The enteric pathogens were confirmed via successful isolation in 93 out of the 412 stool specimens. Fifty-nine bacteria and thirty-six viruses were detected, among which V. parahaemolyticus, Salmonella and noroviruses were the leading etiologic agents. Among different pathogens many showed unique seasonal distribution, while others were common throughout the year. The two most common bacterial pathogens showed exceedingly high level of antimicrobial drug resistance. Finally, we found linkage of V. parahaemolyticus and Salmonella ST genetic variants and frequencies of specific virulence genes but not with drug resistance, further suggesting very wide spread of resistance genes across different unrelated strains of these pathogens.

The predominant enteric diarrheal pathogens detected in this study were V. parahaemolyticus (6.6%), Salmonella (5.6%) and Norovirus (5.3%). The isolation rate of V. parahaemolyticus was close to the 8.0% reported for southeastern China in previous years (Chen et al., 2016) and consistent with earlier report from Shanghai, in which V. parahaemolyticus was the most commonly detected bacterial pathogen (Zhang et al., 2014). However, Lei Jia’s study, which identified pathogens in almost 40% of patients in Beijing, reported calicivirus (16.1%) as the most prevalent pathogen, followed by rotavirus (11.3%), V. parahaemolyticus (5.1%) and Salmonella (3.9%) (Jia et al., 2016). Salmonella was the second most commonly detected EP in our studies and the isolation rate was 5.6%, which was higher than the previous study from Shanghai (0.9%) (Zhang et al., 2014) and Beijing (3.9%) (Jia et al., 2016), however, in all these studies Salmonella remained 2nd most common bacterial EP. Outside of China, comparative epidemiology shows even greater divergence. A Nordic country reported calicivirus, rotavirus and Campylobacter jejuni as the most common pathogens from 2003 to 2007 (Hilmarsdottir et al., 2012). Kenya reported rotavirus and Shigella as the main cause of diarrhea in 2009 to 2011 (Swierczewski et al., 2013). Australian report, ranks norovirus, followed by C. difficile and rotavirus as the most frequent causes of infectious diarrhea in 2007 (Huhulescu et al., 2009). These differences demonstrate that the pathogen spectrum significantly varies in different areas, the possible cause of these differences maybe the different races, diets and sanitation. However, these disparities were likely influenced by different research periods and variety of methods applied for detection. Thus, surveillance of GI pathogens implemented regularly at different study centers around the world will continue provide important updates regarding pathogen distribution.

Our results showed that in Shanghai norovirus remains the leading etiologic agent of viral diarrhea. Specifically, Norovirus GII accounted for 95.5% among the virus positive specimens in our study, consistent with the notion that GII viruses became established as the predominant type responsible for the majority of norovirus gastroenteritis in recent years worldwide (Estevez et al., 2013). Noroviruses cause nearly 200,000 deaths each year among children less than 5 years old in developing countries and efforts are being made to introduce preventative vaccines (Patel et al., 2009; Kim and Kim, 2014). Since, experimental norovirus vaccine studies show strong association between viral genotype and effectiveness of vaccine-induced protection (Atmar et al., 2011), our results support that the focus of vaccine development efforts should be on GII Norovirus group.

The analysis of seasonal distribution of etiological causes showed that there was strong seasonal dependence of enteric pathogen incidence. The epidemic peak of viral infections occurred mainly in winter/early spring whereas the peak of bacterial diarrheas occurred in summer and autumn, which was similar to the studies from other cities in China (Jia et al., 2016; Chi et al., 2017). Interestingly, peak of viral infection corresponded to lowest level of bacterial infections and vice versa, with the exception of November–January, during which incidences of both viral and bacterial infection levels were at their lowest points. The analysis of the seasonal distribution of viral pathogens showed that most outbreaks with low frequency viruses were restricted to a short period of time, which could be a result of a specific viral gene mutation that exploited the gap in population immunity, as typically seen with influenza viruses (Carter and Sanford, 2012; Reperant et al., 2015). In contrast, norovirus was detected in most months of the year; consistent with findings in multiple centers, which showed indiscriminately high frequencies of norovirus infections worldwide (Ahmed et al., 2014).

Among bacterial species we also found some interesting differences in seasonal distribution patterns. V. parahaemolyticus was only found from May to September contrasting with Salmonella detected in most months of the year. Since V. parahaemolyticus is often isolated from seawater and seafood, the consumption of contaminated seafood appears to be one of the leading causes of summer diarrheas in Shanghai and likely other coastal regions. On the other hand Salmonella, as an important foodborne pathogen with wide array of contamination sources accounting for its broad distribution (Campioni et al., 2012; Jackson et al., 2013).

In recent years, increasing antibiotic resistance of clinical isolates, especially MDR has been a major concern for human health, as it often results in prolonged illness and greater risk of death (Canton and Ruiz-Garbajosa, 2011). In this study, we analyzed the resistance profile of the diarrheal bacteria to 11 common antibiotics. All V. parahaemolyticus isolates showed a high level of resistance to cephalosporins (55.6–100.0%), contrary to the results of 2015 Shanghai study, which showed a low drug resistance rate to cephalosporins (Li et al., 2017). Also investigation of V. parahaemolyticus in southeastern China from 2009 to 2013 reported most isolates were sensitive to common antimicrobial agents apart from ampicillin (Chen et al., 2016). Thus, our results indicated the resistance rate to cephalosporins had markedly increased in Shanghai (Elmahdi et al., 2016). Salmonella exhibited high resistance rates to cefuroxime (CXM) and levofloxacin (LVX). However, CXM and LVX are still commonly used in treatment of acute infectious diarrhea. Remarkably, we found the MDR rates were high in all bacteria isolates, including Shigella which demonstrated 100% MDR frequency. The most common resistance combination of V. parahaemolyticus and Salmonella was cephalosporins and quinolone, which are also the most commonly used antibiotics in our region. The bacteria may acquire resistance to antibiotics via mutations in chromosomal genes or by horizontal gene transfer induced by excess antibiotic application. In addition, the spread of drug-resistant genes mediated by plasmids or bacteriophage may also be a potential cause (Blair et al., 2015; Lekunberri et al., 2017). While our study could not identify mechanisms by which the isolates acquired resistance, they showed that the drug resistance was widely and quite uniformly spread across multiple genotypic variants (Table 3), and thus no statistically significant association was found between resistance and ST strain classification. Together, our findings support that antibiotic resistance reached critical level and this needs to be addressed in clinical practice.

The final group of conclusions pertains to genetic diversity and distribution of common virulence genes critical for pathogenicity of V. parahaemolyticus and Salmonella across their different STs. This data set only marks the beginning of longitudinal studies that will help us to dissect trends pathogens’ genetic microevolution overtime. While, ST3 presented the most dominant ST in V. parahaemolyticus, consistent with previous study in Asian countries (Han et al., 2016), it strikingly differs from the predominant types in Maryland, United: ST631 and ST36 (Haendiges et al., 2015) not found in our study. This is not surprising since the origins of V. parahaemolyticus at both sites are linked to Pacific and Atlantic Ocean, respectively, and involve different continents. Future studies, especially from the American West Coast may provide further insights, if the divergence of ST type is linked more to the aquatic or continental location (local micro evolution) and also how this may be further affected by globalization of the seafood industry. The pandemic serotype of V. parahaemolyticus were O3:K6, consistent with the findings from other places worldwide (Ceccarelli et al., 2013; Velazquez-Roman et al., 2014). In terms of virulence, human V. parahaemolyticus isolates detected in this study contained tlh gene a hallmark of virulent V. parahaemolyticus (Banerjee et al., 2014; Chen et al., 2016) and almost equally and uniformly common across STs gene. The ureR gene and trh were both collectively absent. Since, ureR is located immediately upstream of trh, our results further support that while not necessary for virulence, these two virulence-associated genes are genetically linked, and complications introduced by inter-strains sequence heterogeneity might be avoided by detection of the ureR gene (Nilsson and Turner, 2016). Overall, conclusion is that V. parahaemolyticus is largely dominated by one or two STs and serotypes, the serotypes were generally associated with STs of V. parahaemolyticus, none apparent association between genetic diversities, serotypes with its resistance phenotypes was detected in our results, consistent with uniformly wide-spread resistance among all most prevalent ST types found in Shanghai.

Among the 23 Salmonella isolates, the most frequently detected was ST11, followed by ST19 and ST34 in contrast with reported predominant STs of Salmonella isolates were ST8, ST4 and ST3 in America (Dutta et al., 2014). These outcomes reveal important regional differences in Salmonella STs. Serovar Enteritidis was the most frequently isolated followed by Typhimurium, consistent with the data from foodborne outbreaks in America (Andino and Hanning, 2015). Regarding Salmonella virulence genes distribution, SPIs genes were present in almost all isolates, while SPV genes only occurred in 35–44% of the isolates, which demonstrated that the significant variations in pathogenicity among isolates were mainly attributed to the spread of plasmid genes. Furthermore, genetic distribution of virulence factors appears to show stronger link with STs compared with V. parahaemolyticus, consistent with previous reports linking STs with virulence and resistance (Luo et al., 2014; Li et al., 2017). In our study, most ST19 Salmonella isolates were positive for SPV and SPI genes, corresponding patients’ information showing more severe symptoms in ST19-infected patients. This was in contrast with Salmonella typhimurium, which was corresponding to ST19 and ST34 isolates. Meanwhile, all other STs except for ST11 were negative for all SPV genes but all SPI genes, similar to serovars Newport, Thompson, Montevideo, London, Grampian and Give. Finally, the very broad resistance to multiple antibiotics was uniformly spread across various STs and serotypes indicating that the rate of acquiescence of drug resistance is very fast and occurs independent of STs and serotypes. Based on these findings, we recommended the further longitudinal and multi-center studies monitoring the virulence along with genotype of ST classification.

Our study systematically explored the distribution, seasonality, STs, serotypes, antimicrobial susceptibility phenotype and distribution of virulence genes of the pathogens from patients with acute diarrhea in Shanghai in 2016. The results highlighted the regional difference of diarrhea pathogens, confirmed that V. parahaemolyticus, Salmonella and norovirus still presented as the most prevalent pathogens in the region, exhibited the main STs, serotypes, emphasized the serious antibiotic resistance, explored the association of virulence with genetic diversity and serotypes of V. parahaemolyticus and Salmonella isolates. This study would provide useful information for comparing of molecular epidemiology in our region over time and among different regions to guide appropriate therapeutic strategies and monitoring the variation of genotypes of pathogens causing acute diarrheas.

FY, YJ, LY, and JQ contributed to this work equally. CY, MC, YMZ, and HuZ designed and coordinated the study. FY, YJ, LY, JQ, and MG collected specimens and detected the pathogens. YL, HC, YZ, and JZ designed the primers and did the data analysis. FY, ML, HoZ, ZD, YMZ, and HuZ interpreted the data and prepared the manuscript. All the authors approved the submission of the manuscript.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.